src/nonbonded/LJ.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */

#include <stdio.h>
#include <string.h>

#include <cmath>
#include "nonbonded/LJ.hpp"
#include "utils/simError.h"

namespace OpenMD {

  LJ::LJ() : name_("LJ"), initialized_(false), shiftedPot_(false), 
             shiftedFrc_(false), forceField_(NULL) {}

  LJParam LJ::getLJParam(AtomType* atomType) {
    
    // Do sanity checking on the AtomType we were passed before
    // building any data structures:
    if (!atomType->isLennardJones()) {
      sprintf( painCave.errMsg,
               "LJ::getLJParam was passed an atomType (%s) that does not\n"
               "\tappear to be a Lennard-Jones atom.\n",
               atomType->getName().c_str());
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
    
    GenericData* data = atomType->getPropertyByName("LennardJones");
    if (data == NULL) {
      sprintf( painCave.errMsg, "LJ::getLJParam could not find Lennard-Jones\n"
               "\tparameters for atomType %s.\n", atomType->getName().c_str());
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError(); 
    }
    
    LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
    if (ljData == NULL) {
      sprintf( painCave.errMsg,
               "LJ::getLJParam could not convert GenericData to LJParam for\n"
               "\tatom type %s\n", atomType->getName().c_str());
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();          
    }
    
    return ljData->getData();
  }

  RealType LJ::getSigma(AtomType* atomType) {    
    LJParam ljParam = getLJParam(atomType);
    return ljParam.sigma;
  }

  RealType LJ::getSigma(AtomType* atomType1, AtomType* atomType2) {    
    RealType sigma1 = getSigma(atomType1);
    RealType sigma2 = getSigma(atomType2);
    
    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
    string DistanceMix = fopts.getDistanceMixingRule();
    toUpper(DistanceMix);

    if (DistanceMix == "GEOMETRIC") 
      return sqrt(sigma1 * sigma2);
    else 
      return 0.5 * (sigma1 + sigma2);
  }

  RealType LJ::getEpsilon(AtomType* atomType) {    
    LJParam ljParam = getLJParam(atomType);
    return ljParam.epsilon;
  }

  RealType LJ::getEpsilon(AtomType* atomType1, AtomType* atomType2) {    
    RealType epsilon1 = getEpsilon(atomType1);
    RealType epsilon2 = getEpsilon(atomType2);
    return sqrt(epsilon1 * epsilon2);
  }

  void LJ::initialize() {    
    ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
    ForceField::AtomTypeContainer::MapTypeIterator i;
    AtomType* at;

    for (at = atomTypes->beginType(i); at != NULL; 
         at = atomTypes->nextType(i)) {
      
      if (at->isLennardJones())
        addType(at);
    }

    ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
    ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
    NonBondedInteractionType* nbt;

    for (nbt = nbiTypes->beginType(j); nbt != NULL; 
         nbt = nbiTypes->nextType(j)) {
      
      if (nbt->isLennardJones()) {
        
        pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes();
        
        GenericData* data = nbt->getPropertyByName("LennardJones");
        if (data == NULL) {
          sprintf( painCave.errMsg, "LJ::rebuildMixingMap could not find\n"
               "\tLennard-Jones parameters for %s - %s interaction.\n", 
                   atypes.first->getName().c_str(),
                   atypes.second->getName().c_str());
          painCave.severity = OPENMD_ERROR;
          painCave.isFatal = 1;
          simError(); 
        }
    
        LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
        if (ljData == NULL) {
          sprintf( painCave.errMsg,
                   "LJ::rebuildMixingMap could not convert GenericData to\n"
                   "\tLJParam for %s - %s interaction.\n", 
                   atypes.first->getName().c_str(),
                   atypes.second->getName().c_str());
          painCave.severity = OPENMD_ERROR;
          painCave.isFatal = 1;
          simError();          
        }
        
        LJParam ljParam = ljData->getData();

        RealType sigma = ljParam.sigma;
        RealType epsilon = ljParam.epsilon;

        addExplicitInteraction(atypes.first, atypes.second, sigma, epsilon);
      }
    }  
    initialized_ = true;
  }
      

  void LJ::addType(AtomType* atomType){
    RealType sigma1 = getSigma(atomType);
    RealType epsilon1 = getEpsilon(atomType);
    
    // add it to the map:
    AtomTypeProperties atp = atomType->getATP();    

    pair<map<int,AtomType*>::iterator,bool> ret;    
    ret = LJMap.insert( pair<int, AtomType*>(atp.ident, atomType) );
    if (ret.second == false) {
      sprintf( painCave.errMsg,
               "LJ already had a previous entry with ident %d\n",
               atp.ident);
      painCave.severity = OPENMD_INFO;
      painCave.isFatal = 0;
      simError();         
    }
    
    // Now, iterate over all known types and add to the mixing map:
    
    std::map<int, AtomType*>::iterator it;
    for( it = LJMap.begin(); it != LJMap.end(); ++it) {
      
      AtomType* atype2 = (*it).second;

      LJInteractionData mixer;
      mixer.sigma = getSigma(atomType, atype2);
      mixer.epsilon = getEpsilon(atomType, atype2);
      mixer.sigmai = 1.0 / mixer.sigma;
      mixer.explicitlySet = false;

      std::pair<AtomType*, AtomType*> key1, key2;
      key1 = std::make_pair(atomType, atype2);
      key2 = std::make_pair(atype2, atomType);
      
      MixingMap[key1] = mixer;
      if (key2 != key1) {
        MixingMap[key2] = mixer;
      }
    }      
  }
  
  void LJ::addExplicitInteraction(AtomType* atype1, AtomType* atype2, RealType sigma, RealType epsilon){
    
    // in case these weren't already in the map
    addType(atype1);
    addType(atype2);

    LJInteractionData mixer;
    mixer.sigma = sigma;
    mixer.epsilon = epsilon;
    mixer.sigmai = 1.0 / mixer.sigma;
    mixer.explicitlySet = true;

    std::pair<AtomType*, AtomType*> key1, key2;
    key1 = std::make_pair(atype1, atype2);
    key2 = std::make_pair(atype2, atype1);
    
    MixingMap[key1] = mixer;
    if (key2 != key1) {
      MixingMap[key2] = mixer;
    }    
  }
 
  void LJ::calcForce(InteractionData idat) {
    
    if (!initialized_) initialize();
    
    RealType ros;
    RealType rcos;
    RealType myPot = 0.0;
    RealType myPotC = 0.0;
    RealType myDeriv = 0.0;
    RealType myDerivC = 0.0;

    std::pair<AtomType*, AtomType*> key = std::make_pair(idat.atype1, 
                                                         idat.atype2);
    LJInteractionData mixer = MixingMap[key];

    RealType sigmai = mixer.sigmai;
    RealType epsilon = mixer.epsilon;
    

    ros = idat.rij * sigmai;

    getLJfunc(ros, myPot, myDeriv);

    if (shiftedPot_) {
      rcos = idat.rcut * sigmai;
      getLJfunc(rcos, myPotC, myDerivC);
      myDerivC = 0.0;
    } else if (LJ::shiftedFrc_) {
      rcos = idat.rcut * sigmai;
      getLJfunc(rcos, myPotC, myDerivC);
      myPotC = myPotC + myDerivC * (idat.rij - idat.rcut) * sigmai;
    } else {
      myPotC = 0.0;
      myDerivC = 0.0;
    }

    RealType pot_temp = idat.vdwMult * epsilon * (myPot - myPotC);
    idat.vpair += pot_temp;

    RealType dudr = idat.sw * idat.vdwMult * epsilon * (myDeriv - 
                                                        myDerivC)*sigmai;
    
    idat.pot += idat.sw * pot_temp;
    idat.f1 = idat.d * dudr / idat.rij;

    return;

  }
  
  void LJ::getLJfunc(RealType r, RealType &pot, RealType &deriv) {

    RealType ri = 1.0 / r;
    RealType ri2 = ri * ri;
    RealType ri6 = ri2 * ri2 * ri2;
    RealType ri7 = ri6 * ri;
    RealType ri12 = ri6 * ri6;
    RealType ri13 = ri12 * ri;
    
    pot = 4.0 * (ri12 - ri6);
    deriv = 24.0 * (ri7 - 2.0 * ri13);

    return;
  }
  

}
Revision:	1502
Committed:	Sat Oct 2 19:53:32 2010 UTC (14 years, 7 months ago) by gezelter
File size:	10059 byte(s)
Log Message:	Many changes, and we're not quite done with this phase yet.
#	User	Rev	Content
1	gezelter	1471	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Redistributions of source code must retain the above copyright
10			* notice, this list of conditions and the following disclaimer.
11			*
12			* 2. Redistributions in binary form must reproduce the above copyright
13			* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31			*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39			* [4] Vardeman & Gezelter, in progress (2009).
40			*/
41
42			#include <stdio.h>
43			#include <string.h>
44
45			#include <cmath>
46			#include "nonbonded/LJ.hpp"
47			#include "utils/simError.h"
48
49			namespace OpenMD {
50
51	gezelter	1502	LJ::LJ() : name_("LJ"), initialized_(false), shiftedPot_(false),
52			shiftedFrc_(false), forceField_(NULL) {}
53	gezelter	1471
54			LJParam LJ::getLJParam(AtomType* atomType) {
55
56			// Do sanity checking on the AtomType we were passed before
57			// building any data structures:
58			if (!atomType->isLennardJones()) {
59			sprintf( painCave.errMsg,
60			"LJ::getLJParam was passed an atomType (%s) that does not\n"
61			"\tappear to be a Lennard-Jones atom.\n",
62			atomType->getName().c_str());
63			painCave.severity = OPENMD_ERROR;
64			painCave.isFatal = 1;
65			simError();
66			}
67
68			GenericData* data = atomType->getPropertyByName("LennardJones");
69			if (data == NULL) {
70			sprintf( painCave.errMsg, "LJ::getLJParam could not find Lennard-Jones\n"
71			"\tparameters for atomType %s.\n", atomType->getName().c_str());
72			painCave.severity = OPENMD_ERROR;
73			painCave.isFatal = 1;
74			simError();
75			}
76
77			LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
78			if (ljData == NULL) {
79			sprintf( painCave.errMsg,
80			"LJ::getLJParam could not convert GenericData to LJParam for\n"
81			"\tatom type %s\n", atomType->getName().c_str());
82			painCave.severity = OPENMD_ERROR;
83			painCave.isFatal = 1;
84			simError();
85			}
86
87			return ljData->getData();
88			}
89
90			RealType LJ::getSigma(AtomType* atomType) {
91			LJParam ljParam = getLJParam(atomType);
92			return ljParam.sigma;
93			}
94
95			RealType LJ::getSigma(AtomType* atomType1, AtomType* atomType2) {
96			RealType sigma1 = getSigma(atomType1);
97			RealType sigma2 = getSigma(atomType2);
98
99			ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
100	gezelter	1502	string DistanceMix = fopts.getDistanceMixingRule();
101	gezelter	1471	toUpper(DistanceMix);
102
103			if (DistanceMix == "GEOMETRIC")
104			return sqrt(sigma1 * sigma2);
105			else
106			return 0.5 * (sigma1 + sigma2);
107			}
108
109			RealType LJ::getEpsilon(AtomType* atomType) {
110			LJParam ljParam = getLJParam(atomType);
111			return ljParam.epsilon;
112			}
113
114			RealType LJ::getEpsilon(AtomType* atomType1, AtomType* atomType2) {
115			RealType epsilon1 = getEpsilon(atomType1);
116			RealType epsilon2 = getEpsilon(atomType2);
117			return sqrt(epsilon1 * epsilon2);
118			}
119
120			void LJ::initialize() {
121	gezelter	1476	ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
122	gezelter	1471	ForceField::AtomTypeContainer::MapTypeIterator i;
123			AtomType* at;
124
125	gezelter	1476	for (at = atomTypes->beginType(i); at != NULL;
126			at = atomTypes->nextType(i)) {
127	gezelter	1471
128			if (at->isLennardJones())
129			addType(at);
130			}
131
132	gezelter	1476	ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
133	gezelter	1471	ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
134			NonBondedInteractionType* nbt;
135
136	gezelter	1476	for (nbt = nbiTypes->beginType(j); nbt != NULL;
137			nbt = nbiTypes->nextType(j)) {
138	gezelter	1471
139			if (nbt->isLennardJones()) {
140
141	gezelter	1502	pair<AtomType, AtomType> atypes = nbt->getAtomTypes();
142	gezelter	1471
143			GenericData* data = nbt->getPropertyByName("LennardJones");
144			if (data == NULL) {
145			sprintf( painCave.errMsg, "LJ::rebuildMixingMap could not find\n"
146			"\tLennard-Jones parameters for %s - %s interaction.\n",
147			atypes.first->getName().c_str(),
148			atypes.second->getName().c_str());
149			painCave.severity = OPENMD_ERROR;
150			painCave.isFatal = 1;
151			simError();
152			}
153
154			LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
155			if (ljData == NULL) {
156			sprintf( painCave.errMsg,
157			"LJ::rebuildMixingMap could not convert GenericData to\n"
158			"\tLJParam for %s - %s interaction.\n",
159			atypes.first->getName().c_str(),
160			atypes.second->getName().c_str());
161			painCave.severity = OPENMD_ERROR;
162			painCave.isFatal = 1;
163			simError();
164			}
165
166			LJParam ljParam = ljData->getData();
167
168			RealType sigma = ljParam.sigma;
169			RealType epsilon = ljParam.epsilon;
170
171			addExplicitInteraction(atypes.first, atypes.second, sigma, epsilon);
172			}
173			}
174			initialized_ = true;
175			}
176
177
178
179			void LJ::addType(AtomType* atomType){
180			RealType sigma1 = getSigma(atomType);
181			RealType epsilon1 = getEpsilon(atomType);
182	gezelter	1502
183	gezelter	1471	// add it to the map:
184			AtomTypeProperties atp = atomType->getATP();
185	gezelter	1473
186	gezelter	1502	pair<map<int,AtomType*>::iterator,bool> ret;
187			ret = LJMap.insert( pair<int, AtomType*>(atp.ident, atomType) );
188	gezelter	1471	if (ret.second == false) {
189			sprintf( painCave.errMsg,
190			"LJ already had a previous entry with ident %d\n",
191			atp.ident);
192			painCave.severity = OPENMD_INFO;
193			painCave.isFatal = 0;
194			simError();
195			}
196
197			// Now, iterate over all known types and add to the mixing map:
198
199			std::map<int, AtomType*>::iterator it;
200			for( it = LJMap.begin(); it != LJMap.end(); ++it) {
201
202			AtomType* atype2 = (*it).second;
203
204			LJInteractionData mixer;
205			mixer.sigma = getSigma(atomType, atype2);
206			mixer.epsilon = getEpsilon(atomType, atype2);
207			mixer.sigmai = 1.0 / mixer.sigma;
208			mixer.explicitlySet = false;
209
210			std::pair<AtomType, AtomType> key1, key2;
211			key1 = std::make_pair(atomType, atype2);
212			key2 = std::make_pair(atype2, atomType);
213
214			MixingMap[key1] = mixer;
215			if (key2 != key1) {
216			MixingMap[key2] = mixer;
217			}
218			}
219			}
220
221			void LJ::addExplicitInteraction(AtomType* atype1, AtomType* atype2, RealType sigma, RealType epsilon){
222
223			// in case these weren't already in the map
224			addType(atype1);
225			addType(atype2);
226
227			LJInteractionData mixer;
228			mixer.sigma = sigma;
229			mixer.epsilon = epsilon;
230			mixer.sigmai = 1.0 / mixer.sigma;
231			mixer.explicitlySet = true;
232
233			std::pair<AtomType, AtomType> key1, key2;
234			key1 = std::make_pair(atype1, atype2);
235			key2 = std::make_pair(atype2, atype1);
236
237			MixingMap[key1] = mixer;
238			if (key2 != key1) {
239			MixingMap[key2] = mixer;
240			}
241			}
242
243	gezelter	1502	void LJ::calcForce(InteractionData idat) {
244
245	gezelter	1471	if (!initialized_) initialize();
246
247			RealType ros;
248			RealType rcos;
249			RealType myPot = 0.0;
250			RealType myPotC = 0.0;
251			RealType myDeriv = 0.0;
252			RealType myDerivC = 0.0;
253
254	gezelter	1502	std::pair<AtomType, AtomType> key = std::make_pair(idat.atype1,
255			idat.atype2);
256	gezelter	1471	LJInteractionData mixer = MixingMap[key];
257
258			RealType sigmai = mixer.sigmai;
259			RealType epsilon = mixer.epsilon;
260
261	gezelter	1473
262	gezelter	1502	ros = idat.rij * sigmai;
263	gezelter	1471
264			getLJfunc(ros, myPot, myDeriv);
265
266			if (shiftedPot_) {
267	gezelter	1502	rcos = idat.rcut * sigmai;
268	gezelter	1471	getLJfunc(rcos, myPotC, myDerivC);
269			myDerivC = 0.0;
270			} else if (LJ::shiftedFrc_) {
271	gezelter	1502	rcos = idat.rcut * sigmai;
272	gezelter	1471	getLJfunc(rcos, myPotC, myDerivC);
273	gezelter	1502	myPotC = myPotC + myDerivC * (idat.rij - idat.rcut) * sigmai;
274	gezelter	1471	} else {
275			myPotC = 0.0;
276			myDerivC = 0.0;
277			}
278
279	gezelter	1502	RealType pot_temp = idat.vdwMult * epsilon * (myPot - myPotC);
280			idat.vpair += pot_temp;
281	gezelter	1471
282	gezelter	1502	RealType dudr = idat.sw * idat.vdwMult * epsilon * (myDeriv -
283			myDerivC)*sigmai;
284	gezelter	1471
285	gezelter	1502	idat.pot += idat.sw * pot_temp;
286			idat.f1 = idat.d * dudr / idat.rij;
287	gezelter	1471
288			return;
289	gezelter	1473
290	gezelter	1471	}
291
292	gezelter	1472	void LJ::getLJfunc(RealType r, RealType &pot, RealType &deriv) {
293
294	gezelter	1471	RealType ri = 1.0 / r;
295			RealType ri2 = ri * ri;
296			RealType ri6 = ri2 * ri2 * ri2;
297			RealType ri7 = ri6 * ri;
298			RealType ri12 = ri6 * ri6;
299			RealType ri13 = ri12 * ri;
300	gezelter	1472
301	gezelter	1471	pot = 4.0 * (ri12 - ri6);
302			deriv = 24.0 * (ri7 - 2.0 * ri13);
303	gezelter	1472
304	gezelter	1471	return;
305			}
306	gezelter	1472
307	gezelter	1471
308			}